Not sure how academic scene works in your country, but my experience is that you can write a thesis about anything in humanities, if you are able to convince people there's something meaningful in the phenomenon - popcultural studies may be young, but they're only expanding and it would be absolutely doable to make a serious research project on VNs from the perspective of literary studies, game studies, fan studies etc. I even made a small project on VN fan translations for a conference, even though I never expanded it as far as I initially wanted.
I also made my master's thesis on MLP fan porn, in no way a mainstream phenomenon, and it was in sociology, where the burden of showing what you write about is meaningful in the scale of the broader societal issues is a bit higher than in cultural studies. Even so, it's true that there's virtually no academic work on VN in the West - when doing research, I've been literally able to find one book about VNs and their anime adaptation, which wasn't very helpful or particularly interesting BTW. I imagine it's not much better in Japan, as popcultural studies are still very weak there. I'd say there are a few reasons for it:
1. It's an extremely niche medium, that is seriously absent from most people's popcultural knowledge - I think there many very curious aspects of VNs for both cultural studies and marketing, but simply too few people know them well enough to write about them in a meaningful way. Even in the academic world, it's the fans that drive various types' of media presence in the discussion and there's simply too few of us.
2. It's a medium connected to porn, which means it will very likely be picked up by porn studies or by no one. I don't think the stigma connected to porn is that bad in the humanities/social studies nowadays, but once more, you have to first learn about the medium in-depth and see its potential before you can write anything interesting about it. And the idea of VNs being "gross fanservice games for horny teenagers" definitely doesn't help with that.
If I end my leave next year and go back to my academic work, I will surely try to publish something on VN fan translations in English. Maybe will refocus my PhD on it, because the current project surely isn't getting anywhere.